Firstly....I want to ask you a question....are you looking to study Bujinkan, Genbukan, Jinenkan,
or that extremely silly bullshit ala 'Koga Ryu.'

Now, I want to explain something to you...Ninjutsu in terms of the Bujinkan is richly over-used. What we study are 6 Samurai Bujutsu Ryu, and 3 Ninpo Ryu (2 of which Soke himself doesn't largely teach directly for various reasons.)
So you have 6 Samurai Bujutsu Ryu and 1, count it 1, Ninpo Ryu left.....that's why I said, the Ninja thing gets over-used entirely too much when it comes to the Bujinkan.

There are 9 schools, as I've mentioned...they're as follows :

Gyokko Ryu Kosshijutsu (specializes in muscle and nerve attacks via finger drives and the like)
Koto Ryu Koppojutsu (specializes in skeletal structure attacks)
Kukishin Ryu Roikumiuchi (purely battlefield art, taught in both full Yoroi armor, and also unarmored, lots of bit hits and standing grappling)
Gikan Ryu Koppojutsu (branch school from the founder of Gyokko Ryu)
Takagiyoshin Ryu Jutaijutsu (a bodyguard school, with a technique base somewhat similar to that of Daito Ryu)
Shinden Fudo Ryu Dakentaijutsu (another battlefield art, lots of heavy atemi and nasty throws)
Togakure Ryu Ninpo Taijutsu(1 of 3 Ninjutsu Ryu-ha, the only one of which that was fully combative and has a high amount of Densho Waza (written combat techniques) because of that.
Gyokushin Ryu

Gyokushin Ryu Ninpo Taijutsu (a school based around information gathering, and espionage rather than physical combat)
Kumokukure Ryu Ninpo Taijutsu- (same as above, but it's combat techniques are a bit more pronounced- specialized in aerial attacks and offensive Ukemi, as well as a specialization of the Kamayari- a weapon unique to Ninpo)

I have to get back to work, so that's all for now.

Matthius, if you have any questions...feel free to ask here, or to PM me.

There are supposed to be some koryu arts in Japan that include ninjutsu. You need to be clear on what you expect ninjutsu to be though, how do you define it? Conventionally ninjutsu/shinobi jutsu refers to stealth/stealer-in, espionage, geurilla tactics, and so forth. However, Hatsumi Masaaki (a kanji scholar and recognized by the emporer as a national living treasure for his calligraphy) offers an interpretation of the character meaning perseverance. Nowadays, he provides this as a philosophical basis for his martial arts but technically refers to them collectively as Budo Taijutsu.

Refering to our training as "ninjutsu" is slippery ground. As kyoketsu already stated most of what we do is conventional koryu bujutsu; mostly standup striking and grappling. We train several methods of striking, joint locking, throws, groundfighting, and a variety of weapons. It's based in the concept of taijutsu, whole-body feeling. It's very straightforward. Most of it comes from three or four of the nine schools (Gyokko ryu, Takagi Yoshin ryu, Kukishinden ryu), though it's all been sort of blended together into a single cirriculum. Since techniques are often found in many schools, we will usually practice with the "feeling" and strategies of a specific ryu, occasionally from one of the ninjutsu schools.

There are specific "ninjutsu" waza, but usually people don't have the foundations practiced well enough to understand them, and much of the knowledge of these schools is fairly context-specific and not entirely practical today. Why study how to exploit 14th century superstition and methods of infiltrating a medieval Japanese stronghold? There are methodologies found in these schools that are useful in hand-to-hand combat, but this is something that will find its way out of you on its own. The most direct example is refined application of kyojutsu, "the exchange of truth and falsehood," a concept of decieving the opponent in various ways that is found in ANY fighting system in action.

So in a way, we don't do ninjutsu at all. On the other hand, EVERYTHING we do could be considered ninjutsu. Hows that for typical Bujinkan ambiguity? :) Seriously, it's as esoteric or ambigious as you desire to make it.

If you want to learn how to sneak around and perform espionage, there are paramilitary, bodyguard/security, and investigative training centers that will be a much more direct path.

Wastrel, I'm going to explain myself. With google, I've managed to find information on a whole bunch of martial arts. The ones I create topics about, I haven't found anything on. This is why I'm on this website. To dodge people such as you, and learn about the martial arts I missed.